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OpenMiChroM is a Python library for performing chromatin dynamics simulations and analyses. Open-MiChroM uses the OpenMM Python API employing the MiChroM (Minimal Chromatin Model) energy function. The chromatin dynamics simulations generate an ensemble of 3D chromosomal structures that are consistent with experimental Hi-C maps. OpenMiChroM also allows simulations of a single or multiple chromosome chain using High-Performance Computing in different platforms (GPUs and CPUs).
The chromatin dynamics simulations can be performed for different human cell lines, cell phases (interphase to metaphase), and different organisms from DNAzoo. Chromatin subcompartment annotations are available at the NDB (Nucleome Data Bank). Open-MiChroM package receives the chromatin sequence of compartments and subcompartments as input to create and simulate a chromosome polymer model. Examples of running the simulations and generating the in silico Hi-C maps can be found here
- Reference Documentation: Examples, tutorials, and class details.
- Installation Guide: Instructions for installing OpenMiChroM.
- Open-MiChroM Google Group: Ask questions to the OpenMiChroM user community.
- GitHub repository: Download the OpenMiChroM source code.
- Issue tracker: Report issues/bugs or request features.
When using OpenMiChroM to perform chromatin dynamics simulations or analyses, please use this citation.
The OpenMiChroM library can be installed via conda or pip, or compiled from source.
The code below will install OpenMiChroM from conda-forge.
conda install -c conda-forge OpenMiChroMHint
Often, the installation via conda happens to be stuck. If this is the case, it is recommended to update conda/anaconda using the command line below and try to install OpenMiChroM again.
conda update --prefix /path/to/anaconda3/ anacondaThe code below will install OpenMiChroM from PyPI.
pip install OpenMiChroMThe OpenMiChroM library uses OpenMM API to run the chromatin dynamics simulations. These requirements can be met by installing the OpenMM package from the conda-forge channel:
conda install -c conda-forge openmmThe following are libraries required for installing OpenMiChroM: